Leveraging Peptide Sequence Modification to Promote Assembly of Chiral Helical Gold Nanoparticle Superstructures

Chirality of sub-nanometer nanowires/nanobelts

Chirality is a widespread phenomenon in the fields of nature and chemicals, endowing compounds with distinctive chemical and biological characteristics. The conventional synthesis of chiral nanomaterials relies on the introduction of chiral ligands or additives and environmental factors such as solvents and mechanical forces. Sub-nanometer nanowires (SNWs) and sub-nanometer nanobelts (SNBs) are one-dimensional nanomaterials with high anisotropy, nearly 100% atomic exposure ratio and some other distinctive characteristics. In addition to traditional synthesis methods, the intrinsic chirality of SNWs/SNBs can also be achieved by several methods, such as the construction of asymmetric defects and counterion exchange. Chiral SNWs/SNBs have wide application prospects in chiral catalysis, chiral optical devices, chiral drug delivery, chiral liquid crystal materials, chiral sensors, and so on. In this work, we briefly introduce several examples of the origination, amplification, and transfer of the chirality in SNWs/SNBs. This review aims to deepen chirality researchers' understanding of the fundamental origins of intrinsic chirality in SNWs/SNBs and lays the foundation for expanding their potential applications.

Chiral Transfer and Evolution in Cysteine Induced Cobalt Superstructures

Chiral organic additives have unveiled the extraordinary capacity to form chiral inorganic superstructures, however, complex hierarchical structures have hindered the understanding of chiral transfer and growth mechanisms. This study introduces a simple hydrothermal synthesis method for constructing chiral cobalt superstructures with cysteine, demonstrating specific recognition of chiral molecules and outstanding electrocatalytic activity. The mild preparation conditions allow in situ tracking of chirality evolution in the chiral cobalt superstructure, offering unprecedented insights into the chiral transfer and amplification mechanism. The resulting superstructures exhibit a universal formation process applicable to other metal oxides, extending the understanding of chiral superstructure evolution. This work contributes not only to the fundamental understanding of chirality in self-assembled structures but also provides a versatile method for designing chiral inorganic nanomaterials with remarkable molecular recognition and electrocatalytic capabilities.

Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review

Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.

Biosynthesis of metal nanoparticles: Bioreduction and biomineralization

The biosynthesis of metal nanoparticles by plants, bacteria, and cells has been receiving considerable attention in recent years. The traditional synthesis of metal nanoparticles always needed high temperatures, high pressure, and toxic agents. However, the biosynthesis process (including bioreduction and biomineralization) is simpler, safe, economical, and green. The process of biosynthesis can insulate toxic agents, streamline flux, increase the transition efficiency of interactants, and improve the product yield. The biosynthesized metal nanoparticles share similar characteristics with traditional ones, serving as photosensors to achieve light-to-heat/energy transduction, or a drug delivery system. The biosynthetic metal nanoparticles thus could be widely applied in the medical field for disease diagnosis and treatment. It contributed a novel modality for the facile and green synthesis of metal nanoparticles. Increasing studies have been exploring the mechanism for the biosynthesis of metal nanoparticles, devoted to a controllable biosynthesis process. Combined with our previous studies on the biosynthesis of gold nanoparticles with green tea, tumor cells, and cell components, we reviewed the green methods of bioreduction and biomineralization of metal nanoparticles including the internal mechanism, aimed to make a comprehensive introduction to the biosynthesis of metal nanoparticles and relevant biomedical applications, and inspired further research.

Sequence rules for gold-binding peptides

Metal-binding peptides play a central role in bionanotechnology, wherein they are responsible for directing growth and influencing the resulting properties of inorganic nanomaterials. One of the key advantages of using peptides to create nanomaterials is their versatility, wherein subtle changes in the sequence can have a dramatic effect on the structure and properties of the nanomaterial. However, precisely knowing which position and which amino acid should be modified within a given sequence to enhance a specific property can be a daunting challenge owing to combinatorial complexity. In this study, classification based on association rules was performed using 860 gold-binding peptides. Using a minimum support threshold of 0.035 and confidence of 0.9, 30 rules with confidence and lift values greater than 0.9 and 1, respectively, were extracted that can differentiate high-binding from low-binding peptides. The test performance of these rules for categorizing the peptides was found to be satisfactory, as characterized by accuracy = 0.942, F₁ = 0.941, MCC = 0.884. What stands out from the extracted rules are the importance of tryptophan and arginine residues in differentiating peptides with high binding affinity from those with low affinity. In addition, the association rules revealed that positions 2 and 4 within a decapeptide are frequently involved in the rules, thus suggesting their importance in influencing peptide binding affinity to AuNPs. Collectively, this study identified sequence rules that may be used to design peptides with high binding affinity.

Molecular Modulator Approach for Controlling the Length of Chiral 1D Single-Helical Gold Nanoparticle Superstructures

Peptide-based methods have proven useful for constructing helical gold nanoparticle superstructures that exhibit strong plasmonic chiroptical activity. Superstructure syntheses using the amphiphilic peptide conjugate C₁₆-(AYSSGAPPM^oxPPF)₂ typically yield 1D helices with a broad length distribution. In this study, we introduce a molecular modulator approach for controlling helix length. It represents a first step toward achieving narrowly disperse populations of single helices fabricated using peptide-based methods. Varying amounts of modulator, C₁₆-(AYSSGA)₂, were added to C₁₆-(AYSSGAPPM^oxPPF)₂-based single-helix syntheses, resulting in decreased helix length and narrowing of the helix length distribution. Kinetic studies of fiber assembly were performed to investigate the mechanism by which the modulator affects helix length. It was found that the modulator leads to rapid peptide conjugate nucleation and fiber growth, which in turn results in large amounts of short fibers that serve as the underlying scaffold for the single-helix superstructures. These results constitute important advances toward generating monodisperse samples of plasmonic helical colloids.

Single Amino Acid Modifications for Controlling the Helicity of Peptide-Based Chiral Gold Nanoparticle Superstructures

Assembling nanoparticles (NPs) into well-defined superstructures can lead to emergent collective properties that depend on their 3-D structural arrangement. Peptide conjugate molecules designed to both bind to NP surfaces and direct NP assembly have proven useful for constructing NP superstructures, and atomic- and molecular-level alterations to these conjugates have been shown to manifest in observable changes to nanoscale structure and properties. The divalent peptide conjugate, C₁₆-(PEP_Au)₂ (PEP_Au = AYSSGAPPMPPF), directs the formation of one-dimensional helical Au NP superstructures. This study examines how variation of the ninth amino acid residue (M), which is known to be a key Au anchoring residue, affects the structure of the helical assemblies. A series of conjugates of differential Au binding affinities based on variation of the ninth residue were designed, and Replica Exchange with Solute Tempering (REST) Molecular Dynamics simulations of the peptides on an Au(111) surface were performed to determine the approximate surface contact and to assign a binding score for each new peptide. A helical structure transition from double helices to single helices is observed as the peptide binding affinity to the Au(111) surface decreases. Accompanying this distinct structural transition is the emergence of a plasmonic chiroptical signal. REST-MD simulations were also used to predict new peptide conjugate molecules that would preferentially direct the formation of single-helical AuNP superstructures. Significantly, these findings demonstrate how small modifications to peptide precursors can be leveraged to precisely direct inorganic NP structure and assembly at the nano- and microscale, further expanding and enriching the peptide-based molecular toolkit for controlling NP superstructure assembly and properties.

Biomimetic mineralization based on self-assembling peptides

Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.

Chiral inorganic nanomaterials for biological applications

Chiral nanomaterials in biology play indispensable roles in maintaining numerous physiological processes, such as signaling, site-specific catalysis, transport, protection, and synthesis. Like natural chiral nanomaterials, chiral inorganic nanomaterials can also be established with similar size, charge, surface properties, and morphology. However, chiral inorganic nanomaterials usually exhibit extraordinary properties that are different from those of organic materials, such as high g-factor values, broad distribution range, and symmetrical mirror configurations. Because of these unique characteristics, there is great potential for application in the fields of biosensing, drug delivery, early diagnosis, bio-imaging, and disease therapy. Related research is summarized and discussed in this review to showcase the bio-functions and bio-applications of chiral inorganic nanomaterials, including the construction methods, classification and properties, and biological applications of chiral inorganic nanomaterials. Moreover, the deficiencies in existing studies are noted, and future development is prospected. This review will provide helpful guidance for constructing chiral inorganic nanomaterials with specific bio-functions for problem solving in living systems.

A Machine Learning Classification Model for Gold-Binding Peptides

There has been growing interest in using peptides for the controlled synthesis of nanomaterials. Peptides play a crucial role not only in regulating the nanostructure formation process but also in influencing the resulting properties of the nanomaterials. Leveraging machine learning (ML) in the biomimetic workflow is anticipated to accelerate peptide discovery, make the process more resource-efficient, and unravel associations among attributes that may be useful in peptide design. In this study, a binary ML classifier is formulated that was trained and tested on 1720 peptide examples. The support vector machine classifier uses Kidera factors to categorize peptides into one of two groups based on their binding ability. The classifier exhibits satisfactory performance, as demonstrated by various performance metrics. In addition, key variables that bear a huge impact on the model were identified, such as peptide hydrophobicity. As these trends were derived from a large and diverse dataset, the insights drawn from the data are expected to be generalizable and robust. Thus, the presented ML model is an important step toward the rational and predictive peptide design.

Self-Complementary Zwitterionic Peptides Direct Nanoparticle Assembly and Enable Enzymatic Selection of Endocytic Pathways

Supramolecular self-assembly in biological systems holds promise to convert and amplify disease-specific signals to physical or mechanical signals that can direct cell fate. However, it remains challenging to design physiologically stable self-assembling systems that demonstrate tunable and predictable behavior. Here, the use of zwitterionic tetrapeptide modalities to direct nanoparticle assembly under physiological conditions is reported. The self-assembly of gold nanoparticles can be activated by enzymatic unveiling of surface-bound zwitterionic tetrapeptides through matrix metalloprotease-9 (MMP-9), which is overexpressed by cancer cells. This robust nanoparticle assembly is achieved by multivalent, self-complementary interactions of the zwitterionic tetrapeptides. In cancer cells that overexpress MMP-9, the nanoparticle assembly process occurs near the cell membrane and causes size-induced selection of cellular uptake mechanism, resulting in diminished cell growth. The enzyme responsiveness, and therefore, indirectly, the uptake route of the system can be programmed by customizing the peptide sequence: a simple inversion of the two amino acids at the cleavage site completely inactivates the enzyme responsiveness, self-assembly, and consequently changes the endocytic pathway. This robust self-complementary, zwitterionic peptide design demonstrates the use of enzyme-activated electrostatic side-chain patterns as powerful and customizable peptide modalities to program nanoparticle self-assembly and alter cellular response in biological context.

Importance of Substrate-Particle Repulsion for Protein-Templated Assembly of Metal Nanoparticles

We study the protein-directed assembly of colloidal gold nanoparticles on de novo designed protein nanofiber templates. Using sequential assembly on glass substrates, we attach positively charged gold nanoparticles to protein nanofibers engineered to have a high density of negatively charged surface residues. Using a combination of electron and optical microscopy, we measure the density of particle attachment and characterize binding specificity. By varying nanoparticle size and pH of the solution, we explore the importance of charge-dependent particle-fiber and particle-substrate interactions. We find an inverse correlation between particle size and attachment density to protein nanofibers, attributed to the balance between size-dependent electrostatic particle-fiber attraction and particle-substrate repulsion. We show pH-dependent particle attachment density and binding specificity in relation to the protonation fraction of each assembly layer. Finally, we employ hyperspectral scattering microscopy to draw conclusions about particle density and interparticle spacings of optically observable particle assemblies.